How to make a precise bolt hole in a simpler way?
I'd do it almost your way, just skipping a couple of steps..




As you did, knife Project and cut through
Deselect the bottom faces, and E extrude the top faces downard, numerically entering the depth of 0.5 in the 'last operator' panel
Select the top and bottom inner faces, and..
...'Bridge Edge Loops' (you don't need to delete)


However, if your topology is simple enough to stand it, and you wouldn't need to do too much tidying afterwards.. you could just make and duplicate the bolts in the correct dimensions, and cut them all out in a single boolean operation.